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Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity

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MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

Modeling metabolic and signaling pathways in cancer cells

Maria Masid Barcon

Cancer is a leading cause of death in the world, and the mechanisms that underlie this disease are still not completely understood. As cancer develops and progresses, cells undergo a diversity of mutations that sustain their rapid proliferation and the eva ...

EPFL2020

High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuits

Zoe Newell Swank

Cell-free systems have emerged as a versatile platform for constructing complex biological systems from the bottom-up. In particular, they enable the rapid engineering and characterization of gene regulatory networks, a critical cellular subsystem that all ...

EPFL2020

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other t ...

2019

Analysis of cellular and drug action mechanisms in the malaria parasites using systems biology approaches

Anush Chiappino-Pepe

Malaria puts at risk of infection half of the world population and still kills around half a million people every year. The rapid and worrisome rise of drug-resistant malaria parasites hinders the treatment of malaria and calls for a global collaboration t ...

EPFL2018

Microfluidic device combining hydrodynamic and dielectrophoretic trapping for the controlled contact between single micro-sized objects and application to adhesion assays

Philippe Renaud, Arnaud Bertsch, Clémentine Sophie Sarah Lipp

The understanding of cell-cell and cell-matrix interactions via receptor and ligand binding relies on our ability to study the very first events of their contact. Of particular interest is the interaction between a T cell receptor and its cognate peptide-m ...

ROYAL SOC CHEMISTRY2023

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

Oxford University Press2018

Exploring the interplay of molecular pattern and valency for selective interactions at the bio-interface

Kaltrina Paloja

Cell-cell communication is fundamental for immune balance. Multivalent interactions of surface receptors at immune interfaces drive specific communication, with stimulatory and inhibitory signals guiding the immune outcome. Notably, the valency, affinity, ...

EPFL2023

A Three-Dimensional Engineered Cardiac In Vitro Model: Controlled Alignment of Cardiomyocytes in 3D Microphysiological Systems

Philippe Renaud, Fatemeh Navaee

Cardiomyocyte alignment in myocardium tissue plays a significant role in the physiological, electrical, and mechanical functions of the myocardium. It remains, however, difficult to align cardiac cells in a 3D in vitro heart model. This paper proposes a si ...

MDPI2023

CDN1163, an activator of sarco/endoplasmic reticulum Ca2+ ATPase, up-regulates mitochondrial functions and protects against lipotoxicity in pancreatic β-cells

Andreas Wiederkehr

Background and Purpose: High levels of Ca2+ in the endoplasmic reticulum (ER), established by the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA), are required for protein folding and cell signalling. Excessive ER Ca2+ release or decreased SERCA activity i ...

2023

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

Joana Raquel Pinto Vieira

Systems biology is a multidisciplinary field that weaves together all the basic sciences through the use of computational and bioinformatics tools, to provide a more integrative view of the complex molecular interactions taking place within and among cells ...

EPFL2017

Guidelines for Genome-Scale Analysis of Biological Rhythms

Felix Naef, Frédéric Bruno Martin Gachon

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods ...

Sage Publications Inc2017

Phosphoproteomics and morphology of stored human red blood cells treated by protein tyrosine phosphatases inhibitor

Gerardo Turcatti, Benjamin Rappaz, Romain Hamelin, Florence Armand

The process of protein phosphorylation is involved in numerous cell functions. In particular, phosphotyrosine (pY) has been reported to play a role in red blood cell (RBC) functions, including the cytoskeleton organization. During their storage before tran ...

2023

Novel systems biology approaches for design and analysis of palmitoylation networks reveal its regulatory effects on protein stability, activity and localization

Tiziano Dallavilla

Communication and environment sensing are fundamental for the regulation of the majority of the cellular functions. In cells there are dedicated networks that are responsible for signalling, which gives the ability to the cell of sensing the external and i ...

EPFL2017

Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies

Kristina Pan Woodruff

With the advent of high-throughput and genome-wide screening initiatives, there is a need for improved methods for cell-based assays. Current approaches require expensive equipment, rely on large-scale culturing formats not suited for small or rare sample ...

EPFL2017

A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing

Sebastian Maerkl, Kristina Pan Woodruff

Mammalian synthetic biology could be augmented through the development of high-throughput microfluidic systems that integrate cellular transfection, culturing, and imaging. We created a microfluidic chip that cultures cells and implements 280 independent t ...

Nature Research2016

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Julien Racle

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...

EPFL2014

Developing the Biomolecular Screening Facility at the EPFL into the Chemical Biology Screening Platform for Switzerland

Gerardo Turcatti

The Biomolecular Screening Facility (BSF) is a multidisciplinary laboratory created in 2006 at the Ecole Polytechnique Federale de Lausanne (EPFL) to perform medium and high throughput screening in life sciences-related projects. The BSF was conceived and ...

Bentham Science Publishers2014

Systems Biology Approaches for Inflammatory Bowel Disease: Emphasis on Gut Microbial Metabolism

Although the prevalence of main idiopathic forms of inflammatory bowel disease (IBD) has risen considerably over the last decades, their clinical features do not allow accurate prediction of prognosis, likelihood of disease progression, or response to spec ...

Lippincott Williams & Wilkins2014